Summary: Chronic infection with the hepatitis C virus (HCV) is a major cause of cirrhosis, decompensated liver disease and hepatocellular carcinoma (HCC) worldwide. Globally there are an estimated 180 million persons with HCV. In the United States (U.S.), there are 4.1 million persons who are anti-HCV positive, 3.2 million of whom have chronic infection based on the detection of HCV RNA in serum. In 2011, chronic liver disease was the 10th leading cause of death in the U.S. most due to chronic HCV infection. These figures underscore the magnitude and impact that chronic HCV infection has on global and US public health. The natural history of chronic HCV infection has been difficult to study. The protracted and silent course of infection, the absence of large cohorts of persons known to be infected, and the wide variability in outcome are major obstacles to natural history studies. Five to twenty-five percent of HCV-infected persons will develop cirrhosis over a 25-30 year period but some patients remain asymptomatic, without significant liver disease for many decades if not for life. Knowledge of the rate of progression among individuals who have not developed cirrhosis is unknown. An equally important and related issue is the clinical assessment of disease severity. Unfortunately, there are no good laboratory markers of disease severity and liver biopsy, the accepted gold standard for assessing disease severity is imperfect. Non-invasive methods to assess disease severity are highly desirable for the clinicians diagnostic toolbox. The optimal treatment for chronic HCV infection is undergoing a paradigm change with the advent of direct acting antiviral (DAA) agents. For genotype 1 infection response rates now approach 70-75%, close to that of genotypes 2 and 3. The challenging group of patients to treat are those who have failed a prior course of peginterferon and ribavirin and those with advanced disease. Therapeutic options for these subjects are improving but few studies have been conducted in these patient populations. Thus studies using newer, safer and more effective therapies are urgently needed for these sub-populations with chronic HCV infection. Hypotheses/problems addressed: 1) Define the host, viral and environmental factors that determine the natural history and outcome of HCV infection. To address this problem, we have created a large database of untreated patients with chronic HCV (n700) and have analyzed this database to identify factors that affect the natural history of chronic HCV infection. We have published 4 studies on this cohort, identifying clinical factors and candidate genes associated with fibrosis progression. Autoimmune hepatitis sometimes occurs in patients with chronic hepatitis C but presents difficult diagnostic and management challenges. To address the former issue we used the database to identify patients with co-existent autoimmune hepatitis and chronic hepatitis C to identify clinical and laboratory characteristics that can distinguish them from patients with chronic hepatitis C alone. The factors associated with hepatic decompensation among patients with advanced chronic hepatitis C are not well understood. Recently, it was reported that the prevalence of hepatitis E was 21% among the U.S. population. In endemic regions, hepatitis E is associated with acute on chronic liver failure. Thus, we investigated the role of hepatitis E in hepatic decompensation in the U.S. We retrospectively tested samples from patients with and without hepatic decompensation enrolled in a former study-the HALT-C study. Both the prevalence and incidence of hepatitis E was similar in patients with and without hepatic decompensation suggesting that hepatitis E does not contribute to decompensation among patients with hepatitis C in the U.S. Finally, we are validating the usefulness of a new technology, ultrasound elastography, to non-invasively assess hepatic fibrosis. Results revealed that the device has a 96% accuracy for prediction of cirrhosis. Studies are ongoing to compare transient elastography with other non-invasive markers of fibrosis. Our goal is to develop a series of blood and imaging test that will obviate the need for liver biopsy in most patients with chronic HCV infection. 2) Develop and evaluate novel, safer and more effective therapies for chronic viral hepatitis. Management options for non-responders to peginterferon and ribavirin are limited. At the LDB, we have explored multiple options including, low dose, long term peginterferon, peginterferon and ribavirin plus SAMe, and peginterferon in combination with high dose ribavirin all with limited success. We have recently initiated a trial evaluating two new oral, direct acting antiviral agents- asunaprevir and daclatasvir either together or in combination with peginterferon and ribavirin to treat prior non-responders to peginterferon and ribavirin. Thirty-five subjects have been enrolled and the study is ongoing. 3. Elucidate the viral pathogenesis of chronic HCV infection and mechanisms of action of anti-viral therapy The conduct of clinical trials over the last 30 years has allowed the LDB to acquire invaluable clinical material (patient serum, liver tissue and lymphophocytes) to which state of the art laboratory techniques can be applied to address issues of the pathogenesis of HCV infection and the mechanisms of action of antiviral therapy. In association with the above clinical study using asunaprevir and daclatasvir we are seeking to answer three critical questions surrounding therapy of chronic hepatitis C: (1) what happens to the expression of interferon stimulated genes (ISG) following suppression of viral replication (2) can interferon responsiveness be restored in non-responders after suppression of viral replication and (3) why do patients with cirrhosis respond less compared to those without cirrhosis. To address these questions, we are comparing the relative expression level of ISGs before and after suppression of viremia with potent direct acting antiviral agents and focusing on genes that regulate the innate immune response.